Variant Omicron: in France, symptoms, incubation

The Omicron variant of Covid circulates almost exclusively in France and its BA.5 sublineage is still ubiquitous in September 2022. It is the most contagious variant of Covid compared to the previous ones. What are the symptoms (cough, loss of taste...)? What is the incubation period?

[Updated September 9, 2022 at 11:49 a.m.] Appeared in South Africa in November 2021, the variant Omicron two coronaviruses 'circulates in such a way almost exclusively in France and its sub-lineage BA.5 is currently ubiquitous ' indicate Public Health France in the epidemiological point of September 8. BA.5 represents 95% of the interpretable sequences. The proportion of BA.4 decreases and represents 4% of the interpretable sequences. Omicron also accounts for the majority of contamination Covid in the world. It's the most contagious variant of Covid compared to the previous ones (Alpha, Delta...). And you can contract it twice -even if the risk of reinfection by Omicron is even higher if one has been contaminated before by another variant (Delta...). The Omicron variant includes five sublineage s BA.1, BA.2, BA.3, BA.4 et BA.5 . The symptoms the most common are the fatigue, cough, fever, headache and sore throat. Definition , incubation time, symptoms common with Omicron, contagion, effectiveness of vaccines, treatment ... All about the variant Omicron.

What is the Omicron variant?

The Omicron variant was first reported to WHO by South Africa on November 24, 2021. The UK has been with the Norway and the Denmark one of the first countries on the European continent affected by the Omicron variant. L' epidemic started in London in december 2021 then arrived in France . This variant belongs to the Pango lineage B.1.1.529 . 'It's a variant that has a great name of mutations' , explained Dr. Maria Van Kerkhove of the World Health Organization on November 25, 2021. Among these specific mutations: the deletion 69/70 and substitutions K417N , S371L-S373P et Q493R.

The gradual appearance of sub-lineages is an expected phenomenon.

In a December 2021 Opinion, the French Scientific Council recalled that 'most of the mutations are observed on the Spike protein ( about 30 ), other mutations are also observed in the N protein gene and in the NSP6 gene, mutations that may have a impact on the level of multiplication of the virus ' . According Public Health France , them three major characteristics of Omicron are her high transmissibility, immune escape and lower severity.

The variant Omicron includes the five sublineages BA.1, BA.2, BA.3, BA.4 and BA.5 . 'Given the intensity of the circulation of Omicron in the world, genetic diversification within this variant and the progressive appearance of sub-lineages is an expected phenomenon ' reassured Public Health France in the analysis of variants published at the end of April. The Omicron variant has been classified as 'special concern' or VOC about l'OMS on November 26, 2021. There are three types of variants depending on the WHO ranking : them VOC (variant of concern such as Delta, Alpha, Beta, Gamma and Omicron variants), the VOI (variant to follow) and the VUM (variant under surveillance like the XD variant).

What are the BA4 and BA5 variants?

The BA.4 and BA.5 sublineages have been identified in early April 2022 . These two sub-lineages, mainly detected in South Africa , are quite similar to BA.2 but their Spike protein additionally has the L452R mutation (which was responsible for the increased transmissibility of the Delta variant) which explains why they are closely monitored by the health authorities. In mid-June, the BA.5 sub-lineage became the majority in France and still is in September (95% of Covid tests): the BA.4 remains in the minority (4% of tests). The ECDC, based on these genetic characteristics, classified these sub-lineages into variants to follow (VOI) and asked that they be carefully monitored .

How many cases of the Omicron variant in France?

Sequencing data confirm ubiquity d'Omicron in France and its BA.5 sublineage. In a city, BA.5 (all sub-lineages combined) represented 95% of sequences interpretable during the Flash S33 investigation ( 08/16 ). The proportion of BA.4 (all sublines included) during Flash surveys decreases, with 4% of sequences interpretable during Flash S33 compared to 6% during Flash S32. The detection of mutations in position L452 by screening tests has stabilized at high levels (93%), in connection with the circulation of BA.5.

  Circulation of variants of concern in France
Circulation of variants of concern in France as of August 8, 2022

From first identified cases of Omicron in France, one case in Vendée, another in the Haut-Rhin confirmed by the ARS of the Grand Est region in December 2021, a case in Ile-de-France, Seine et Marne declared by  l' Ile-de-France Regional Health Agency .

  Omicron variant sublineages during Flash surveys (EMERGEN)
Sublineages of the Omicron variant during Flash surveys (EMERGEN)-August 2022

The viral load would decrease after 6 days.

How many days are you contagious with Omicron?

According to' study by Japanese researchers published in January 2022, vaccinated cases of Omicron would be contagious for a maximum of 10 days after their diagnosis or the onset of their symptoms. The amount of viral RNA (which can be likened to the ' charge viral ') is highest 3 to 6 days after diagnosis or 3-6 days after onset of symptoms , then gradually decreased over time . According to studies reported by Public Health France , 'Omicron is about 3 times more transmissible than Delta' . His BA2 sub-lineage was ' more contagious (+30%) (than BA1, editor's note) ' informed Professor Arnaud Fontanet on France Inter on March 14. The BA.5 is even more so. ' Omicron replicates extremely rapidly in primary cultures of nasal epithelial cells , even more so than Delta, which replicated itself faster than any previously characterized variants' confirmed English researchers in a analysis published at the end of December . Its transmissibility would be increased because it uses an input channel extra in the cells 'Omicron is able to efficiently enter cells in a TMPRSS2-independent manner (classical pathway, editor's note), via the endosomal pathway. We speculate that this allows Omicron to infect a greater number of cells in the respiratory epithelium, which allows it to be more infectious at lower exposure doses, and enhanced intrinsic transmissibility.' the scientists said. On the other hand it would be 'less likely to replicate in the lungs' reducing the risk of serious illness.

What is the incubation period of Omicron?

The incubation time of the Omicron variant is shorter than that of previous variants of the original Covid: 'We are faced with a variant (Omicron, editor's note) which has a duration (incubation, editor's note), before the onset of symptoms, which went from five to three days' said Professor Yazdan Yazdanpanah of the Scientific Council on BFM-TV on January 2.

What are the symptoms of the Omicron variant?

The report of the symptoms observed in people affected by Omicron comes from data from Public Health France and from an English study published by The Lancet in April 2022, carried out on more than 60,000 volunteers. The clinical presentation of Omicron infections differed from circulating variants previously with less severe forms . omicron provoke less respiratory distress that Delta car il affects the lungs less . The first cases also showed less loss of taste or smell as we have seen with the Covid cases contaminated by the initial virus of Sars-Cov-2 and the Alpha or Delta variants. What seems to change with the BA4 and BA5 variants . 'The probability of presenting loss of taste, loss of smell but also nausea, vomiting and diarrhea is higher for cases positive for variants of BA.4 and BA.5' reports Santé Publique France in its variant risk analysis published in June 2022. study Swedish has also highlighted cases odynophagia acute in people infected with Omicron ( pain felt when swallowing and sore throat) .

  • fatigue
  • cough
  • fever
  • headaches
  • myalgia
  • gorge disease
  • runny nose
  • runny nose
  • headache
  • sore throat
  • sneezing
  • persistent cough and hoarse voice
  Omicron symptoms
Comparison of symptoms Omicron BA1 (present at the end of 2021 in France) with BA4 and BA5 which progresses in June 2022

How long do symptoms last?

According to the cases analyzed by Santé Publique France, the duration of symptoms is on average 4 days in people infected with Omicron, 3 days in those vaccinated with a booster dose. This duration is a little longer for people contaminated by lineages BA4 and BA5: 7 days on average, according to figures from Public Health France.

What are the risks of reinfection with Omicron?

.The Omicron variant is characterized by increased transmissibility and 'significant' immune escape . 'Escape of the Omicron immune response is also associated with reinfection rates for Omicron (following prior infection by another variant) higher than for previously circulating variants' indicated Public Health France.

Why is this variant called Omicron?

Like Alpha, Beta, Delta, Gamma... Omicron is the name of a letter of the Greek alphabet (the 15th), the naming system' more accessible to a non-scientific public ' and ' non stigmatizing “set up to baptize the genetic lines of Sars-CoV-2, explains the WHO . The Greek alphabet has 24 letters. The 13th and 14th letters were not assigned to a variant , the WHO not having yet indicated for what reason.

1 Alpha
two Beta
3 Gamma
4 Delta
5 Epsilon
6 Zeta
7 And
8 Theta
9 Iota
10 Kappa
eleven Lambda
12 In
13 Not
14 KSI/Xi
fifteen Omicron

How effective are vaccines?

If the Omicron variant quickly replaced the Delta variant in the world (and in particular in France), it is partly because it is more contagious but also because he further escapes immunity whether after having had Covid or after vaccination . 'While the emergence of Omicron has been marked by significant vaccine escape, vaccination remains an essential tool to mitigate the impact of SARS-CoV-2' confirms Santé Publique France in its risk analysis of the July 6 variants. A modeling study estimates that vaccination has reduced the number of deaths from COVID-19 worldwide by 63% in the year since its introduction . The effectiveness of vaccines for prevent severe forms and, to a lesser extent, Omicron-related infections, as well as increase in this protection following a booster dose, have been demonstrated by several studies, recalls the health agency. Vaccination and/or a previous covid infection would allow a faster elimination of the virus and in fact a reduction in the contagiousness of the positive person. It is however more possible to catch up with the Covid after being infected with the Omicron variant than with the previous variants. The duration of protection begins to really decrease after 6 months of vaccination (last dose). A french study published in July 2022 estimated that the effectiveness of the booster dose in preventing the risk of hospitalization was 85% during the period of the predominant Delta variant and 81% during the Omicron period (81% with Pfizer / 85% with Moderna) . The efficiency rate fell to 72% more than 3 months after the booster. Faced with the BA4 and BA5 variants, 'the new seroneutralization data confirm the decrease in the effectiveness of post-vaccination antibodies' indicates Public Health France on August 10. One of the consequences is a shorter duration of protection: 5.5 months after the third dose for BA.5 versus 11.5 months for the index strain (Wuhan) . However, a third dose of Pfizer vaccine has been shown to increase the spectrum of antibodies produced and improve cross-protection against BA.5. This cross-protection against BA.5 is even more effective in people vaccinated and previously infected with BA.2

Rate of protection against severe Omicron forms (hospitalization) 1 month after vaccination fifty% 64% 81%
3 months after vaccination 72%
Protection rate against symptomatic infection Omicron 1 month after vaccination 70%
3 months after vaccination fifty%

What is the origin of the Omicron variant?

The Omicron variant was first reported to WHO by South Africa on November 24, 2021. The first known confirmed infection at Omicron in South Africa was from a sample collected on November 9, 2021. The Omicron variant was also detected at Botswana in samples collected on November 11, 2021.

Test: how do you know if you are contaminated with Omicron?

'The effectiveness of diagnostic tests (PCR or antigenic) does not appear to be reduced for Omicron' a confirmed by Santé Publique France in June 2022. The screening strategy has evolved in France to focus on the search for mutations specific to each variant. To date, the indicators monitored are the presence of the E484K mutation (A1), the presence of mutations en position L452 (C1) and the presence of a mutation associated with Omicron ( del69-70 and/or K417N and/or S371L-S373P and/or Q493R, D1) . The screening results from all the regions of metropolitan France and all the DROMs indicate a dominance of Omicron and its sub-lines carrying mutations in position L452.

Is it less dangerous?

Diffusion of the Omicron variant has been associated with significant decrease in hospitalization rate compared to the other variants, which has made it possible to limit its impact on public health. 'This lower severity is partly driven by the pre-existing immunity in the population, which remains protective against severe forms' explains Public Health France. South African and Scottish data suggested a 70-80% reduction in risk of hospitalization for Omicron versus Delta and the English data a reduction of 50-70%. This lesser danger would come from the fact that the Omicron variant attacks the pulmonary system less.  Omicron 'gives less severe clinical forms because it multiplies more in the upper airways and less in the lower airways, giving less pneumopathy (that Delta, ndlr) ' confirmed le Pr Arnaud Fontanet, member of the Scientific Council, on BFM-TV Monday, January 10. 'The Omicron variant sends patients to intensive care less' declared the Minister of Health Olivier Véran that same day. He 'causes shorter hospital stays for new patients than for those infected with previous variants' . According to him, those hospitalized will have oxygen needs for three to four days before he can be discharged from the hospital. However, the variant Omicron being very contagious , many people hospitalized because of Covid are positive for this variant.

  Proportion of suspected Omicron among confirmed cases, patients newly hospitalized for COVID-19 by type of hospitalization and deceased patients, by calendar week, S48-2021 to S03-2022, France
Proportion of suspected Omicron among confirmed cases, patients newly hospitalized for COVID-19 by type of hospitalization and deceased patients, by calendar week, S48-2021 to S03-2022, France

What are the treatments against Omicron?

Treatments for an infection with the Omicron variant do not differ from a classic Covid infection (paracetamol for headache, etc.). In contrast, monoclonal antibodies that may be given to some patients do not appear to be effective against Omicron . ' Studies on the effectiveness of monoclonal antibodies show a neutralizing activity retained for three monoclonal antibodies with broad neutralizing activity (Sotrovimab, S2X259 and S2H97) but of a reduction in the effectiveness of others' reports Santé Publique France on May 18. According to analyzes by researchers from the Pastor Institute published in December of nine monoclonal antibodies used clinically or in the preclinical development phase, six completely lose their antiviral activity , and the other three are 3 to 80 times less effective against Omicron compared to Delta. The evaluation of the efficacy of monoclonal antibodies against BA.5 compared to BA.2 gave similar results for Evusheld, Imdevimab, Bebtelovimab but decreased efficacy for Sotrovimab, Public Health France reported Aug. 18. The three antivirals tested (Remdesivir, Molnupiravir and Nirmatrelvir) retained the same efficacy against BA.4 and BA.5 as against the index strain (Wuhan).

How to protect yourself from Omicron?

The prevention rules against the new Omicron variant are identical to those of the original Sars-Cov-2:

The vaccination: WHO recommends accelerating Covid vaccination coverage as quickly as possible, especially among populations designated as high priority who are unvaccinated or not yet fully vaccinated.

Barrier gestures: masks, physical distancing, indoor space ventilation, crowd avoidance, hand hygiene...

Screening and isolation: Widely use diagnostic tests in the event of symptoms or before an event, including in vaccinated persons: antigenic tests or self-tests as close as possible to the event. And isolate yourself when you're positive.

Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: a prospective observational study from the ZOE COVID Study. 7 avril 2022.

Analysis of available data on possible reinfections with SARS-CoV-2 from the SIDEP database March 31, 2022. Data as of March 20, 2022. Santé Publique France.

Covid-19: First estimates of the place of Delta and Omicron variants in patients hospitalized at AP-HP from December 1, 2021 to January 4, 2022. January 10, 2022. AP-HP.

The SARS-CoV-2 variant, Omicron, shows rapid replication in human primary nasal epithelial cultures and efficiently uses the endosomal route of entry. Thomas P. Peacock1. Department of Infectious Disease, Imperial College London, UK, W2 1PG

Opinion of the Scientific Council COVID-19 December 16, 2021. December 17, 2021.

Update on the SARS-CoV-2 variant Omicron (B.1.1.529). French Public Health. November 26, 2021

French health authorities are monitoring possible cases of people with the Omicron variant on French territory. Ministry of Health. November 28, 2021

Enhancing Readiness for Omicron (B.1.1.529): Technical Brief and Priority Actions for Member States World Health Organization HQ 28 Novembre 2021

A new variant detected in several southern African countries. November 26, 2021.

Frequently asked questions about the B.1.1.529 mutated SARS-CoV-2 lineage in South Africa. National Institute for communicable diseases. 25 novembre 2021.

Focused COVID-19 Media Monitoring Nepal. WHO. 26 November 2021.